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- PDB-6a5r: RNA polymerase II elongation complex stalled at SHL(-2) of the nu... -

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Entry
Database: PDB / ID: 6a5r
TitleRNA polymerase II elongation complex stalled at SHL(-2) of the nucleosome
Components
  • (DNA (198-MER)) x 2
  • (DNA-directed RNA polymerase ...Polymerase) x 3
  • (RNA polymerase II ...) x 4
  • (RNA polymerase subunit ...) x 4
  • DNA-directed RNA polymerases I, II, and III subunit RPABC3RNA polymerase
  • Histone H2A type 1-B/E
  • Histone H2B type 1-J
  • Histone H3.3H3F3A
  • Histone H4
  • RNA (5'-R(P*UP*CP*UP*CP*GP*UP*GP*CP*CP*UP*G)-3')
KeywordsTRANSCRIPTION/RNA/DNA / nucleosome / chromatin / RNA polymerase / TRANSCRIPTION / TRANSCRIPTION-RNA-DNA complex
Function / homologyRNA polymerase Rpb2, OB-fold / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerase subunit, RPB6/omega / Nucleic acid-binding, OB-fold / DNA-directed RNA polymerase RPB5 subunit, eukaryote/virus / RNA polymerases N / 8 Kd subunits signature. / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / Histone H4, conserved site / RNA polymerase, subunit H/Rpb5, conserved site ...RNA polymerase Rpb2, OB-fold / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerase subunit, RPB6/omega / Nucleic acid-binding, OB-fold / DNA-directed RNA polymerase RPB5 subunit, eukaryote/virus / RNA polymerases N / 8 Kd subunits signature. / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / Histone H4, conserved site / RNA polymerase, subunit H/Rpb5, conserved site / Archaeal RpoH /eukaryotic RPB5 RNA polymerase subunit / RNA polymerases, subunit N, zinc binding site / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase subunit RPB10 / DNA-directed RNA polymerase, subunit RPB6 / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / Histone H2A, C-terminal domain / Histone H2A conserved site / Pol II subunit B9, C-terminal zinc ribbon / CENP-T/Histone H4, histone fold / RPB5-like RNA polymerase subunit superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase subunit/transcription factor S / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, insert domain superfamily / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / RNA polymerase Rpb4/RPC9, core / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase, N-terminal / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase, beta subunit, conserved site / HRDC-like superfamily / Histone H2A/H2B/H3 / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 2 / RNA polymerase, beta subunit, protrusion / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 5 / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase, RBP11-like dimerisation domain / Histone-fold / RNA polymerase, RBP11-like subunit / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase, subunit omega/K/RPB6 / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase Rpb2, domain 2 / Centromere kinetochore component CENP-T histone fold / C-terminus of histone H2A / Histone H2A signature. / Histone H4 signature. / Eukaryotic RNA polymerase II heptapeptide repeat. / Histone H3 signature 1. / Histone H2B signature. / RNA polymerases D / 30 to 40 Kd subunits signature. / Histone H3 signature 2. / RNA polymerases M / 15 Kd subunits signature. / RNA polymerase beta subunit / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase Rpb1, domain 2 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase RBP11 / RNA polymerase Rpb1, funnel domain superfamily / Rpb4/RPC9 superfamily / RNA polymerase Rpb1, domain 7 superfamily / Core histone H2A/H2B/H3/H4 / RNA polymerase Rpb2, domain 6 / S1 RNA binding domain / RNA polymerase Rpb3/RpoA insert domain / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / Transcription factor S-II (TFIIS) / RNA polymerase Rpb5, C-terminal domain / RNA polymerase Rpb6 / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases N / 8 kDa subunit / RNA polymerases M/15 Kd subunit / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase Rpb8 / RNA polymerase Rpb5, N-terminal domain / RNA polymerase Rpb4 / Archaeal RpoK/eukaryotic RPB6 RNA polymerase subunit / RNA polymerase Rpb7, N-terminal / RNA polymerases K / 14 to 18 Kd subunits signature.
Function and homology information
Specimen sourceHomo sapiens (human)
Komagataella phaffii (fungus)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 8.7 Å resolution
AuthorsKujirai, T. / Ehara, H. / Fujino, Y. / Shirouzu, M. / Sekine, S. / Kurumizaka, H.
CitationJournal: Science / Year: 2018
Title: Structural basis of the nucleosome transition during RNA polymerase II passage.
Authors: Tomoya Kujirai / Haruhiko Ehara / Yuka Fujino / Mikako Shirouzu / Shun-Ichi Sekine / Hitoshi Kurumizaka
Abstract: Genomic DNA forms chromatin, in which the nucleosome is the repeating unit. The mechanism by which RNA polymerase II (RNAPII) transcribes the nucleosomal DNA remains unclear. Here we report the ...Genomic DNA forms chromatin, in which the nucleosome is the repeating unit. The mechanism by which RNA polymerase II (RNAPII) transcribes the nucleosomal DNA remains unclear. Here we report the cryo-electron microscopy structures of RNAPII-nucleosome complexes in which RNAPII pauses at the superhelical locations SHL(-6), SHL(-5), SHL(-2), and SHL(-1) of the nucleosome. RNAPII pauses at the major histone-DNA contact sites, and the nucleosome interactions with the RNAPII subunits stabilize the pause. These structures reveal snapshots of nucleosomal transcription, in which RNAPII gradually tears DNA from the histone surface while preserving the histone octamer. The nucleosomes in the SHL(-1) complexes are bound to a "foreign" DNA segment, which might explain the histone transfer mechanism. These results provide the foundations for understanding chromatin transcription and epigenetic regulation.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 25, 2018 / Release: Oct 3, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Oct 3, 2018Structure modelrepositoryInitial release
1.1Oct 24, 2018Structure modelData collection / Database referencescitation / citation_author_citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
1.2Nov 14, 2018Structure modelData collection / Database referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

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Assembly

Deposited unit
A: DNA-directed RNA polymerase subunit
B: DNA-directed RNA polymerase subunit beta
C: RNA polymerase II third largest subunit B44, part of central core
D: RNA polymerase II subunit B32
E: RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III
F: RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III
G: RNA polymerase II subunit
H: DNA-directed RNA polymerases I, II, and III subunit RPABC3
I: DNA-directed RNA polymerase subunit
J: RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III
K: RNA polymerase II subunit B12.5
L: RNA polymerase subunit ABC10-alpha
P: RNA (5'-R(P*UP*CP*UP*CP*GP*UP*GP*CP*CP*UP*G)-3')
T: DNA (198-MER)
N: DNA (198-MER)
a: Histone H3.3
b: Histone H4
c: Histone H2A type 1-B/E
d: Histone H2B type 1-J
e: Histone H3.3
f: Histone H4
g: Histone H2A type 1-B/E
h: Histone H2B type 1-J
hetero molecules


Theoretical massNumber of molelcules
Total (without water)748,60332
Polyers748,05623
Non-polymers5489
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)119700
ΔGint (kcal/M)-836
Surface area (Å2)231280

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Components

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DNA-directed RNA polymerase ... , 3 types, 3 molecules ABI

#1: Protein/peptide DNA-directed RNA polymerase subunit / Polymerase / DNA-directed RNA polymerase subunit Rpb1


Mass: 194107.422 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R4Y0, DNA-directed RNA polymerase
#2: Protein/peptide DNA-directed RNA polymerase subunit beta / Polymerase / DNA-directed RNA polymerase subunit Rpb2


Mass: 139746.094 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4QZQ7, DNA-directed RNA polymerase
#9: Protein/peptide DNA-directed RNA polymerase subunit / Polymerase


Mass: 13612.320 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: F2QPE6

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RNA polymerase II ... , 4 types, 4 molecules CDGK

#3: Protein/peptide RNA polymerase II third largest subunit B44, part of central core / RNA polymerase II third largest subunit Rpb3


Mass: 34216.293 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R7L2
#4: Protein/peptide RNA polymerase II subunit B32 /


Mass: 20622.980 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R2U9
#7: Protein/peptide RNA polymerase II subunit / / RNA polymerase II subunit Rpb7


Mass: 18802.625 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R9A1
#11: Protein/peptide RNA polymerase II subunit B12.5 /


Mass: 13832.896 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R3Z5

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RNA polymerase subunit ... , 4 types, 4 molecules EFJL

#5: Protein/peptide RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III /


Mass: 24962.680 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R3P8
#6: Protein/peptide RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III /


Mass: 17803.588 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R1V1
#10: Protein/peptide RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III /


Mass: 8554.064 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R009
#12: Protein/peptide RNA polymerase subunit ABC10-alpha /


Mass: 7862.048 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: F2QMI1

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Protein/peptide , 5 types, 9 molecules Haebfcgdh

#8: Protein/peptide DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA polymerase / RNA polymerase subunit ABC14.5 / common to RNA polymerases I / II / and III


Mass: 16249.220 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R273
#16: Protein/peptide Histone H3.3 / H3F3A


Mass: 15643.262 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Gene: H3F3A, H3.3A, H3F3, PP781, H3F3B, H3.3B / Production host: Escherichia coli (E. coli) / References: UniProt: P84243
#17: Protein/peptide Histone H4 /


Mass: 11676.703 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human)
Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4
Production host: Escherichia coli (E. coli) / References: UniProt: P62805
#18: Protein/peptide Histone H2A type 1-B/E / Histone H2A / Histone H2A.2 / Histone H2A/a / Histone H2A/m


Mass: 14447.825 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2AB, H2AFM, HIST1H2AE, H2AFA / Production host: Escherichia coli (E. coli) / References: UniProt: P04908
#19: Protein/peptide Histone H2B type 1-J / Histone H2B / Histone H2B.1 / Histone H2B.r / H2B/r


Mass: 14217.516 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2BJ, H2BFR / Production host: Escherichia coli (E. coli) / References: UniProt: P06899

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RNA chain , 1 types, 1 molecules P

#13: RNA chain RNA (5'-R(P*UP*CP*UP*CP*GP*UP*GP*CP*CP*UP*G)-3')


Mass: 3436.050 Da / Num. of mol.: 1 / Source: (synth.) synthetic construct (others)

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DNA chain , 2 types, 2 molecules TN

#14: DNA chain DNA (198-MER)


Mass: 60869.977 Da / Num. of mol.: 1 / Source: (synth.) synthetic construct (others)
#15: DNA chain DNA (198-MER)


Mass: 61406.918 Da / Num. of mol.: 1 / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 9 molecules

#20: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Formula: Zn / Zinc
#21: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Formula: Mg / Magnesium

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: RNA polymerase II elongation complex stalled at SHL(-2) of the nucleosome
Type: COMPLEX
Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19
Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Komagataella phaffii (fungus) / Strain: GS115 / ATCC 20864
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
1Gautomatch0.56particle selection
2SerialEMimage acquisition
4Gctf1.06CTF correctionper-particle CTF
7UCSF Chimeramodel fitting
9PHENIXmodel refinement
10Cootmodel refinement
11RELION2.1initial Euler assignment
12RELION2.1final Euler assignment
13RELION2.1classification
14RELION2.13D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 8.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 8798 / Symmetry type: POINT
Atomic model buildingRef protocol: RIGID BODY FIT / Ref space: REAL

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